Abstract: RAPD marker is the most widely adopted molecular marker in forest genetic studies. The main reason is that this kind of markers can be obtained without any DNA sequence information about the studying material before hand. So it is especially suitable for the organism which little molecular study has been carried on. We can design primers arbitratily according to a common rule and the experiment process is relatively simple compared with other kinds of markers, such as RFLP and SSR. But this kind of marker has a fatal shortcoming, if the reaction condition is not suitable for the studying material, it gives out very flexible bands and cant be repeated. So the suitable amplification condition is critical to RAPD analysis. In this paper, the influencing factor on RAPD experiment was analyzed, such as the annealing temperature, the Mg2+ 2]concentration, the template concentration and so on. An optimized protocol especially suitable for forest trees was put forward through a series of experiments. Accord